chr10-68304213-C-T

Variant names:

• chr10-68304213-C-T
• rs7067601
• NM_022129.4:c.84+2548G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022129.4(PBLD):​c.84+2548G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,152 control chromosomes in the GnomAD database, including 47,823 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47823 hom., cov: 33)
• Consequence: PBLD NM_022129.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 1 publications found

Genes affected

PBLD (HGNC:23301): (phenazine biosynthesis like protein domain containing) Enables identical protein binding activity. Involved in maintenance of gastrointestinal epithelium; negative regulation of SMAD protein signal transduction; and negative regulation of transforming growth factor beta receptor signaling pathway. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022129.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBLD	NM_022129.4	MANE Select	c.84+2548G>A		intron	N/A	NP_071412.2	P30039-1
	PBLD	NM_001033083.2		c.84+2548G>A		intron	N/A	NP_001028255.1	P30039-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBLD	ENST00000358769.7	TSL:5 MANE Select	c.84+2548G>A		intron	N/A	ENSP00000351619.2	P30039-1
	PBLD	ENST00000309049.8	TSL:1	c.84+2548G>A		intron	N/A	ENSP00000308466.4	P30039-1
	PBLD	ENST00000880160.1		c.84+2548G>A		intron	N/A	ENSP00000550219.1

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119751 AN: 152034 Hom.: 47791 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.804

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.788 AC: 119839 AN: 152152 Hom.: 47823 Cov.: 33 AF XY: 0.784 AC XY: 58291 AN XY: 74388

African (AFR) AF: 0.669 AC: 27727 AN: 41460

American (AMR) AF: 0.776 AC: 11857 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2788 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4396 AN: 5188

South Asian (SAS) AF: 0.748 AC: 3608 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8364 AN: 10590

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58383 AN: 68032

Other (OTH) AF: 0.806 AC: 1699 AN: 2108

Alfa AF: 0.832 Hom.: 26792

Bravo AF: 0.780

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.83
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7067601; hg19: chr10-70063970;